One question, regarding folders--can I move my "Books" folder into the first directory which opens upon tapping "folders" to make my books more quickly accessible?

In short, yes. First there is a set of built in options what to have as a root folder of internal memory (books, /database/media/books ). Second, if that's not enough, you can reference any folders you want via "favourite folders" feature. Check /database/system/PRSPlus/folders.cfg.sample file. (you have to remove ".sample" and enable "favorite folders" via PRS+ settings menu for this file to work)

Note: everything in PRS+ is case sensitive! "books" is not the same as "Books".

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I'm also wondering if this firmware can be used in conjunction with the Sony Reader Library software or Calibre software?

It's fully compatible with standard software and hence also with Calibre.